From chemistry-request@ccl.net Fri Jul 12 05:35:07 1991
Date: Thu, 11 Jul 1991 21:40:58 PDT
From: "W. Todd Wipke" <wipke@SECS.UCSC.EDU>
To: chemistry@ccl.net
Subject: re: Chemical Taxonomy
Status: R
>David States
>National Center for Biotechnology Information / National Library of Medicine
writes:
>Which raises the question: do you really want a taxonomy, or would you
>in fact want an efficient subgraph matching and lookup algorithm? A
>taxonomy implies a statitic, hierarchical classification of the data, but
>different users of a chemical database almost certainly have different
>applications and different views in mind.
Indeed, the question in my mind is for what do you want the taxonomy?
Typically, taxonomy requires a hierarchy of decision criteria, and for
multipurpose use, one wants different orderings. To take an extreme
position, I would say that taxonomy was for manual systems because
the human mind was limited to a few principles of organization. Taxonomy
has been most successful in chemistry in the Beilstein classification
system. The principle of neighborhood is better for many purposes.
What is the primary goal you have in mind?
-Todd Wipke
Wipke@secs.ucsc.edu
From chemistry-request@ccl.net Fri Jul 12 10:58:58 1991
Date: Fri, 12 Jul 91 14:42:47 GMT
From: jpj@lotus.medicine.rochester.edu (Jeffrey P. Jones)
To: Chemistry@ccl.net
Subject: Self Consistent Reaction Field Program?
Status: R
Hello,
Does anyone have a self consistent reaction field program that
can be used with G90 or GAMESS?
##############################################################################
Jeffrey P. Jones
U. of Rochester
Department of Pharmacology
601 Elmwood Ave.
Rochester, NY 14642
internet jpj@lotus.medicine.rochester.edu
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
From chemistry-request@ccl.net Fri Jul 12 15:17:01 1991
Date: Fri, 12 Jul 91 14:01:51 CDT
From: liberte@ncsa.uiuc.edu (Daniel LaLiberte)
To: chemistry@ccl.net, wipke@SECS.UCSC.EDU
Subject: re: Chemical Taxonomy
Status: R
Todd Wipke writes:
> Indeed, the question in my mind is for what do you want the taxonomy?
> Typically, taxonomy requires a hierarchy of decision criteria, and for
> multipurpose use, one wants different orderings.
I asked about taxonomies to learn more about different classification
schemes. I hadn't heard about the "neighborhood" concept which sounds
like a valuable alternative. What I really need is a way to describe
the properties of chemical structures and the relationships between
those properties. Strictly hierarchical taxonomies would be rather
limited I expect, but that's all I guessed would be out there.
I will be adapting whatever classification schemes I come across to
an object-oriented framework. The OO language I am using includes
multiple inheritance, which appears to be a necessary feature for
chemistry applications. The chemistry tool we are building will support
runtime extensions of the builtin chemistry class library so that
specialists will not be limited by whatever we decide should be in the
builtin library.
Knowledge encoded in each class will tell how to check whether a
certain property exists (if it is a property class) or how to calculate
additional attributes if a given property exists. Related properties
may be in a subclass-superclass relationship, or sibling subclasses of
another superclass, or other possible relationships. One of the
limitations of object-oriented frameworks is that higher-order kinds of
relationships are often difficult or impossible to express in the
language. So figuring out what kinds of relationships are appropriate
for chemistry is a way for me to explore language concepts that will be
required to express these relationships.
I am also interested in classifications of other aspects of chemistry
besides chemical structures (molecules and complexes) - such as
reaction types, types of reaction sequences, and more mundane, though
highly complex things like visualization of simulations and
experimental and theoretical research projects, plans, and results.
liberte@ncsa.uiuc.edu
(217) 244-0785
Daniel LaLiberte
National Center for Supercomputing Applications
152 Computing Appliations Building
605 East Springfield Avenue
Champaign, IL 61820
From chemistry-request@ccl.net Fri Jul 12 19:21:22 1991
Date: Fri, 12 Jul 1991 18:12 EST
From: LONCHARICH_RICHARD_J@LILLY.COM
Subject: dynamics of proteins
To: chemistry@ccl.net
Status: R
I am interested in recent references for molecular
dynamics studies of protein dynamics as a function
of temperature and/or solvent. For example, a series of
classical experimental papers by Frauenfelder et al
(Nature 1979, 280,558-563; PNAS 1982,79,4967-4971).
study the metmyoglobin protein by x-ray diffraction at
several different temperatures. Also Wong, Zheng, and
McCammon (Chem Phys Lett 1989,154,151-154) have used
molecular dynamics to study the atomic motion of tuna
ferrocyctochrome C in SPC/E water from low temperatures
to room temperature.
I would appreciate receiving any references or preprints of molecular
dynamics simulations or any experimental work of proteins
studied at several different temperatures and/or in several different
solvents (ie, CCL4, methanol, water).
Thanks for your help!
================================================
Richard J. Loncharich =
Eli Lilly and Company =
Lilly Corporate Center =
Indianapolis, IN 46285-0403 =
=
Internet: loncharich_richard_j@lilly.com =
================================================
From: LONCHARICH RICHARD J (MCVAX0::RX82788)
To: FOREIGN TRANSPORT ADDRESSEE (MCDEV1::IN%"chemistry@ccl.net")